Just an update in case anyone else comes across this thread with a similar issue. Finally got round to getting the fuel tank and air box off this weekend. Synced and cleaned the throttle bodies. Issue resolved immediately - so after 8 months or so and having been in checked by two seperate mechanics (one holding it for over 2 weeks and unable to fix) it was as simple as that.
Pretty unbelieveable and slightly peeved as at the second garage, I said on the phone 'have you synced and cleaned the throttle bodies' and was told this would not be the issue and if it was it would have been picked up by the diagnostics (no idea what diagnostic there is outside actually stripping the bike down and attaching a manometer to the throttle body - but hey I am no expert.)

Haha.. at the peak of irritation this did cross my mind! (Also saw a brand new Street Triple for £125 per month which was tempting...)
But yea PC sounds like a good idea tbh and my thinking had arrived at a similar point. I am going to run through the basics myself when I have time (which at the moment is never - maybe I can spend Xmas day in the garage!) Then probably look at doing this next year.
Was thinking about getting a Yoshimura exhaust fitted, i figure I can justify the expense slightly more having saved on maintenance

Interesting read. I would assume though that vapor lock would occur when the engine is shut down regardless of whether the ignition is still on? Which is not the case here. I will see if fiddling with the killswitch does anything. tbh i never use it and it is always just off with the key.
Its such a niggling issue that i have left it for ages. Just made me crap myself a few weeks back when I left the petrol station having to sustain throttle to keep it idling, tried to beat the lights at a junction and whilst shifting down, the engine cut out, leaving me stranded in the middle of the junction (for like 2.5 seconds, but with lights all changing feels longer)
I guess one fix is when I turn the ignition off just leave it to cool down. Shouldn't be too hard in this weather!

Hi all,
So over the past 6 or so months I have been having an issue starting the bike when it is hot (+80 degrees) This only occurs when warm and when the ignition is turned off fully. If I kill the engine and restart it starts just fine. When it is hot and the power is turned off - the bike will not idle, I can get it to go with some throttle, but this is risky as it will still drop below 1kRPM if this is not maintained. I have had no time to really investigate this myself so finally I thought I would drop it off at motorcycle repair shop. After 1 week and lots of phone calls it is not solved. I have asked them to email over what they have tested and received this:
"Just to confirm that the following has been undertaken on your bike. Firstly the battery was fully charged and the spark plugs replaced. After speaking to Yamaha technical they suggested that a number of the bikes temperature sensors be checked to ensure that the temperature differential was correct, this has been completed & no issues found. This results in the bike starting fine when cold and with application of a bit of throttle when warm.At this point Yamaha technical has suggested that the next stage is to strip the bike and investigate the wiring loom. As the bike is now out of warranty this cost would be passed onto yourself, we initially estimate that this investigation could take 3-4hrs minimum which would be charged at £75hr + VAT." - (Plugs were checked and cleaned and battery fully charged when the issue first appeared and I had told them this!)
Now I do not want to pay £75 x 4 for possibly no resolution, but looking at forums I did see that some people had luck fixing this with either a throttle body sync or by flashing the ECU with the latest stock version. When I said this to the shop they said 'throttle body sync' would have been picked up with the diagnostic tool and that they 'cannot download the latest ECU from yamaha' anymore.
Does this sound right? Does anyone know a dealer in the London area that can reflash the ECU with the latest stock version?
Also AFAIK the throttle bodies do not have any diagnostics to detect the vacuum (could be wrong.)
So again looks like this was a waste of time and I will have to set some time aside to investigate myself. Any advice appreciated.

Been a while, this made me laugh though - out of curiosity I asked a main dealer in London about costs of replacing brake pads and headstock bearings (Yea I know I should do it myself but I been really busy lately! and am being pretty lazy - I have the parts and my local garage will do the lot for £100) This is their response:
"The cost for parts with labour is £457.81 inc VAT."
"Do you have a breakdown of how you arrived at £457.81? Off the top of my head; OEM bearings cost £25-35, brake pads cost £15-£30, so if we are saying the top end for parts is £95 and labour cost is £90 ph, - that comes out at 4 hour job?"
"The labour is 3 hours with a cost of £75 ph plus VAT
PADS £82.32 +VAT In stock
BEARINGS £74.19 +VAT in stock"
Not sure about anyone here but I have never seen brake pads at £82 or headstock bearings for £74

Welcome, hopefully you will have better luck with this one, These expensive 125's are big targets, most bikes I hear about being stolen are in this category. (well for every 600cc something or other I hear about 4 or 5 125's going missing.)

Just to close this; turns out the negative lead from the battery was oxidised (under the insulation) I assume changing the battery pushed it over the edge somehow. So guess it is a case of adding 2 and 2 and getting 6 really. (or my fault for assuming the error code was accurate!)

So after testing, the battery does loose charge after 48 hours.
Got the mottobat replacement worked great!
Now I have a new powersource I figure, why not install some extras. So I removed tank, ran wire from battery underneath/next to tank, out near air scoop and up to handlebars. Test everything, works fine, put everything back together. Great.
So before riding I thought I would do an extended test, start up bike with everything on. Sitting for 3-4 mins, shudders to a stop...
Now displays error code 12 > malfunction with the crankshaft position sensor.
Removed tank, checked connections, checked fuses, removed additional items I installed. Still nothing but fault code. On top of this my alarm went a bit mad, with ignition on it now rearms itself and goes off, after messing about it seems to have stopped working completely!
I have flicked through service manual, not had time to test everything, If anyone has any thoughts or initial advice let me know!

My two cents: If it is essentially resetting and performing same actions as when you turn the ignition on, I would guess that a connection to the speedo was loose or corroded. (Maybe check the cable guide is not snagging the wire?) Not sure how that could link to acceleration, unless it is the sudden jolt moving the wire or something. Perhaps as a test turn on the ignition, the go full lock either way a few times and see if this causes the meter to reset?
Also maybe a long shot but have you tested the battery (assuming you have no issues starting the bike, so guess it is working correctly!)